Screen capture from a satellite of an area near Masyaf, Hama province Syria where the Syrian Scientific Studies and Research Center reportedly maintains a chemical weapons facility. (Google maps)

The Syrian Foreign Ministry filed a pair of complaints with the United Nations against Israel on Thursday, hours after Israeli warplanes allegedly struck a facility in northwestern Syria where the regime of Bashar Assad is said to have stockpiled chemical weapons and missiles.

In letters to the UN Security Council and UN Secretary-General Antonio Guterres, Syria accused Israel of “repeated aggressions” against Damascus and of “systematic behavior with the aim of protecting Jabhat al-Nusra [the Nusra Front] and ISIS [Islamic State] terrorists.”

The Assad regimes alleged Israel was acting on behalf of “terrorist groups which are carrying out its aggressive agenda and in response to the great achievements made by the Syrian Arab army and its allies in their war against terrorism.

Syria said that any attack against its regime forces “forms a direct support to terrorism, taking into account that the Syrian Arab army is fighting terrorism on behalf of the entire world.”

The Syrian Foreign Ministry called on the Security Council to take “decisive measures to put an end to such flagrant attacks,” according to a report in the Syrian state news agency SANA.

The Syrian army confirmed Thursday morning that a military site near Masyaf was bombed, saying the attack was carried out by Israeli jets and killed two people.

The target was apparently a Scientific Studies and Research Center (CERS) facility in the northern Hama region; CERS is a Syrian government agency that Western officials have long associated with the production of chemical weapons.

“Israeli warplanes fired several rockets from the Lebanese airspace at 02:42 a.m. on Thursday targeting one of the Syrian military posts near Massyaf, killing two army personnel and causing material damage to the site,” the Syrian army said in a statement carried by SANA.

The Syrian military said the attack was “a desperate attempt to raise the collapsed morale” of the Islamic State group “after the sweeping victories achieved by the Syrian Arab Army” and affirmed Israel’s “direct support” for IS and “other terrorist organizations.” It warned it could have “dangerous repercussions.”

Unconfirmed Lebanese reports said Israel also struck a convoy belonging to the Hezbollah terror group in Lebanon. Opposition sources quoted by Israel Radio said the airstrike in Syria destroyed weapons stores including chemical-tipped missiles that were to be delivered to Hezbollah.

There was no comment from the Israeli military on any of the reports.

Defense Minister Avigdor Liberman leads a faction meeting of his Yisrael Beytenu party at the Knesset on July 10, 2017. (Yonatan Sindel/Flash90)

Israel isn’t looking to intervene in the Syrian conflict, the defense minister said, but indicated the Air Force would continue to hit Iran-backed Hezbollah military targets there as necessary.

In May, Liberman said the IDF only carries out raids in Syria for three reasons: when Israel comes under fire, to prevent arms transfers, and to avert a “ticking timebomb,” namely to thwart imminent terror attacks on Israel by groups on its borders.

Syrian opposition forces have in recent months claimed the Masyaf site, and other CERS facilities, have been working on a joint projects with Iranian specialists to develop chemical weapons capability for missiles.

A senior member of the Syrian opposition, citing security officials still working for the regime at the time, told The Times of Israel in 2014 that Assad’s forces were stockpiling chemical substances and missiles carrying chemical warheads at the site, which was not made available to international inspectors tasked with ensuring the destruction of the weapons.

In April the Trump administration placed sanctions on hundreds of CERS employees following a chemical attack on the Syrian rebel-held city of Khan Sheikhoun that killed dozens of civilians, including children. On Wednesday, a report by a UN war crimes commission said it had clear evidence that the Syrian regime was behind the attack and that it had used sarin nerve gas.

Israel has for years been widely believed to have carried out airstrikes on advanced weapons systems in Syria — including Russian-made anti-aircraft missiles and Iranian-made missiles — as well as Hezbollah positions, but it rarely confirms such operations on an individual basis.

In August a former commander of Israel’s air force said that it had carried out dozens of airstrikes on weapons convoys destined for the Hezbollah over the past five years. The remarks by Maj. Gen. Amir Eshel revealed for the first time the scale of the strikes, which are usually neither confirmed nor denied by the IAF.

The most famous Israeli strike in Syria took place almost exactly 10 years ago, on September 6, 2007, when IAF aircraft bombed a suspected nuclear reactor in Deir Ezzor.

Israel has largely stayed out of the fray during the six-year-long civil war in neighboring Syria, but has repeatedly said it will act to prevent Hezbollah from acquiring advanced weapons.

Hezbollah fired more than 4,000 rockets on Israeli communities during its latest war with Israel in 2006. Since Tuesday, tens of thousands of Israeli soldiers have been staging a mock 10-day war against Hezbollah in northern Israel, marking the IDF’s largest exercise in nearly 20 years, the army announced Monday, amid tensions over growing Iranian influence in Syria and Lebanon.

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